R CMD build wiped my computer
Hi Martin, I think this is the most likely reason given that the name in the DESCRIPTION file does NOT have a version number. Even so, it is very easy to misname a file and then delete it/change its name (as I've done here) and I hope current versions of R would not cause this problem. Perhaps Fedora should not use ~ as its back up file suffixes? Cheers, Jarrod
On 28 Jul 2010, at 11:41, Martin Maechler wrote:
Jarrod Hadfield <j.hadfield at ed.ac.uk> on Tue, 27 Jul 2010 21:37:09 +0100 writes:
Hi, I ran R (version 2.9.0) CMD build under root in Fedora (9). When it tried to remove "junk files" it removed EVERYTHING in my local account! (See below).
Can anyone tell me what happened,
the culprit may lay here:
* removing junk files unlink MCMCglmm_2.05/R/ residuals.MCMCglmm.R ~
where it seems that someone (you?) have added a newline in the filname, so instead of 'residuals.MCMCglmm.R~' you got 'residuals.MCMCglmm.R ~' and the unlink / rm command interpreted '~' as your home directory. But I can hardly believe it. This seems explanation seems a bit doubtful to me.. ...
and even more importantly if I can I restore what was lost.
well, you just get it from the backup. You do daily backups, do you? Regards, Martin Maechler, ETH Zurich
Panickingly,
Jarrod
[jarrod at localhost AManal]$ R CMD build MCMCglmm_2.05 * checking for file 'MCMCglmm_2.05/DESCRIPTION' ... OK * preparing 'MCMCglmm_2.05': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * Installing *source* package ?MCMCglmm? ... ** libs g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g - pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c MCMCglmm.cc -o MCMCglmm.o MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, int*, int*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, double*, int*, int*, int*, int*, double*, double*, double*, int*, double*, bool*, double*, double*, int*, int*, int*, int*, int*, double*, int*, int*, int*, double*, double*, double*, int*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*)?: MCMCglmm.cc:228: warning: ?pvLS? may be used uninitialized in this function MCMCglmm.cc:227: warning: ?pvLL? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?Lrv? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?pmuL? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?pvL? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?LambdaX? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?bv_tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?bv? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?A? may be used uninitialized in this function MCMCglmm.cc:86: warning: ?dimG? may be used uninitialized in this function MCMCglmm.cc:228: warning: ?AlphainvS? may be used uninitialized in this function MCMCglmm.cc:227: warning: ?AlphainvL? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?alphalocation_tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?alphalocation? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?alphazstar? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?alphapred? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?alphaastar? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?muAlpha? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?Alphainv? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?tXalpha? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?Xalpha? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?linky_orig? may be used uninitialized in this function MCMCglmm.cc:228: warning: ?tYKrinvYS? may be used uninitialized in this function MCMCglmm.cc:228: warning: ?LambdaS? may be used uninitialized in this function MCMCglmm.cc:227: warning: ?tYKrinvYL? may be used uninitialized in this function MCMCglmm.cc:227: warning: ?LambdaLU? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?tYKrinvY? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?tYKrinv? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?ILY? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?tY? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?Y? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?I? may be used uninitialized in this function MCMCglmm.cc:228: warning: ?alphaS? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?alphaMME? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?alphaM? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?XtmKRinv? may be used uninitialized in this function MCMCglmm.cc:227: warning: ?alphaL? may be used uninitialized in this function MCMCglmm.cc:227: warning: ?L? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?alphaastar_tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?dev? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?astar_tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?Worig? may be used uninitialized in this function gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_add.c -o cs_add.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_addR.c -o cs_addR.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_amd.c -o cs_amd.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_cbind.c -o cs_cbind.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_chol.c -o cs_chol.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_cholsol.c -o cs_cholsol.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_compress.c -o cs_compress.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_counts.c -o cs_counts.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_cov2cor.c -o cs_cov2cor.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_cumsum.c -o cs_cumsum.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_dcmvnorm.c -o cs_dcmvnorm.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_dfs.c -o cs_dfs.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_directsum.c -o cs_directsum.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_directsumupdate.c -o cs_directsumupdate.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_dmperm.c -o cs_dmperm.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_dmvnorm.c -o cs_dmvnorm.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_droptol.c -o cs_droptol.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_dropzeros.c -o cs_dropzeros.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_dupl.c -o cs_dupl.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_entry.c -o cs_entry.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_ereach.c -o cs_ereach.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_etree.c -o cs_etree.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_fkeep.c -o cs_fkeep.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_gaxpy.c -o cs_gaxpy.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_happly.c -o cs_happly.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_house.c -o cs_house.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_inv.c -o cs_inv.o cs_inv.c: In function ?cs_inv?: cs_inv.c:9: warning: ?irow? may be used uninitialized in this function cs_inv.c:9: warning: ?icol? may be used uninitialized in this function gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_invR.c -o cs_invR.o cs_invR.c: In function ?cs_invR?: cs_invR.c:9: warning: ?irow? may be used uninitialized in this function cs_invR.c:9: warning: ?icol? may be used uninitialized in this function gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_ipvec.c -o cs_ipvec.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_kroneckerA.c -o cs_kroneckerA.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_kroneckerAupdate.c -o cs_kroneckerAupdate.o cs_kroneckerAupdate.c: In function ?cs_kroneckerAupdate?: cs_kroneckerAupdate.c:5: warning: unused variable ?Cp? gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_kroneckerH.c -o cs_kroneckerH.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_kroneckerI.c -o cs_kroneckerI.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_kroneckerIupdate.c -o cs_kroneckerIupdate.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_leaf.c -o cs_leaf.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_load.c -o cs_load.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_lsolve.c -o cs_lsolve.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_ltsolve.c -o cs_ltsolve.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_lu.c -o cs_lu.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_lusol.c -o cs_lusol.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_malloc.c -o cs_malloc.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_maxtrans.c -o cs_maxtrans.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_multiply.c -o cs_multiply.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_norm.c -o cs_norm.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_omega.c -o cs_omega.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_omegaupdate.c -o cs_omegaupdate.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_permute.c -o cs_permute.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_pinv.c -o cs_pinv.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_post.c -o cs_post.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_print.c -o cs_print.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_pvec.c -o cs_pvec.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_qr.c -o cs_qr.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_qrsol.c -o cs_qrsol.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_rCinvwishart.c -o cs_rCinvwishart.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_rR.c -o cs_rR.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_randperm.c -o cs_randperm.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_reach.c -o cs_reach.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_rinvwishart.c -o cs_rinvwishart.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_rwishart.c -o cs_rwishart.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_scatter.c -o cs_scatter.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_scc.c -o cs_scc.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_schol.c -o cs_schol.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_sortdv.c -o cs_sortdv.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_spsolve.c -o cs_spsolve.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_sqr.c -o cs_sqr.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_symperm.c -o cs_symperm.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_tdfs.c -o cs_tdfs.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_tmultiplyupdate.c -o cs_tmultiplyupdate.o cs_tmultiplyupdate.c: In function ?cs_tmultiplyupdate?: cs_tmultiplyupdate.c:16: warning: unused variable ?Cx? gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_transpose.c -o cs_transpose.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_updown.c -o cs_updown.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_usolve.c -o cs_usolve.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_util.c -o cs_util.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c cs_utsolve.c -o cs_utsolve.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dcutopints.c -o dcutopints.o g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g - pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c inverseA.cc -o inverseA.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c lpzF.c -o lpzF.o g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g - pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rIW.cc -o rIW.o g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g - pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rbv.cc -o rbv.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rtnorm.c -o rtnorm.o g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g - pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rtnormR.cc -o rtnormR.o g++ -m64 -shared -L/usr/local/lib64 -o MCMCglmm.so MCMCglmm.o cs_add.o cs_addR.o cs_amd.o cs_cbind.o cs_chol.o cs_cholsol.o cs_compress.o cs_counts.o cs_cov2cor.o cs_cumsum.o cs_dcmvnorm.o cs_dfs.o cs_directsum.o cs_directsumupdate.o cs_dmperm.o cs_dmvnorm.o cs_droptol.o cs_dropzeros.o cs_dupl.o cs_entry.o cs_ereach.o cs_etree.o cs_fkeep.o cs_gaxpy.o cs_happly.o cs_house.o cs_inv.o cs_invR.o cs_ipvec.o cs_kroneckerA.o cs_kroneckerAupdate.o cs_kroneckerH.o cs_kroneckerI.o cs_kroneckerIupdate.o cs_leaf.o cs_load.o cs_lsolve.o cs_ltsolve.o cs_lu.o cs_lusol.o cs_malloc.o cs_maxtrans.o cs_multiply.o cs_norm.o cs_omega.o cs_omegaupdate.o cs_permute.o cs_pinv.o cs_post.o cs_print.o cs_pvec.o cs_qr.o cs_qrsol.o cs_rCinvwishart.o cs_rR.o cs_randperm.o cs_reach.o cs_rinvwishart.o cs_rwishart.o cs_scatter.o cs_scc.o cs_schol.o cs_sortdv.o cs_spsolve.o cs_sqr.o cs_symperm.o cs_tdfs.o cs_tmultiplyupdate.o cs_transpose.o cs_updown.o cs_usolve.o cs_util.o cs_utsolve.o dcutopints.o inverseA.o lpzF.o rIW.o rbv.o rtnorm.o rtnormR.o -L/usr/lib64/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading Loading required package: lattice
Attaching package: 'Matrix'
The following object(s) are masked from package:tensorA :
norm
The following object(s) are masked from package:stats :
contr.SAS, contr.helmert, contr.poly, contr.sum, contr.treatment, xtabs
The following object(s) are masked from package:base :
rcond
** help *** installing help indices
Building/Updating help pages for package 'MCMCglmm'
Formats: text html latex example BTdata text html latex BTped text html latex Ddivergence text html latex example Dexpressions text html latex Dtensor text html latex example KPPM text html latex example MCMCglmm text html latex example MCMCglmmPackage text html latex PlodiaPO text html latex PlodiaR text html latex PlodiaRB text html latex Ptensor text html latex example SShorns text html latex Tri2M text html latex example at.level text html latex example at.set text html latex example commutation text html latex example evalDtensor text html latex example inverseA text html latex example knorm text html latex example krzanowski.test text html latex example kunif text html latex example leg text html latex example list2bdiag text html latex example mult.memb text html latex example plot.MCMCglmm text html latex plotsubspace text html latex example posterior.cor text html latex example posterior.evals text html latex example posterior.mode text html latex example predict.MCMCglmm text html latex prunePed text html latex rIW text html latex example rbv text html latex example residuals.MCMCglmm text html latex rtnorm text html latex example sir text html latex example sm2asreml text html latex example spl text html latex example summary.MCMCglmm text html latex ** building package indices ... * DONE (MCMCglmm) * creating vignettes ... OK * cleaning src * removing junk files unlink MCMCglmm_2.05/R/ residuals.MCMCglmm.R ~ unlink MCMCglmm_2.05/R/.DS_Store unlink MCMCglmm_2.05/R/prunePed.R unlink MCMCglmm_2.05/R/commutation.R~ unlink MCMCglmm_2.05/R/rtnorm.R~ unlink MCMCglmm_2.05/R/KPPM.R~ unlink MCMCglmm_2.05/R/cs_inversion.c~ unlink MCMCglmm_2.05/R/posterior.cor.R unlink MCMCglmm_2.05/R/Ddivergence.R~ unlink MCMCglmm_2.05/R/posterior.evals.R unlink MCMCglmm_2.05/R/rbv.R~ unlink MCMCglmm_2.05/R/rbv.R unlink MCMCglmm_2.05/R/plot.prior.R~ unlink MCMCglmm_2.05/R/predict.MCMCglmm.R unlink MCMCglmm_2.05/R/sm2asreml.R~ unlink MCMCglmm_2.05/R/Lweib.R~ unlink MCMCglmm_2.05/R/plot.MCMCglmm.R unlink MCMCglmm_2.05/R/krzanowski.test.R unlink MCMCglmm_2.05/R/Fdivergence.R~ unlink MCMCglmm_2.05/R/sir.R~ unlink MCMCglmm_2.05/R/summary.MCMCglmm.R unlink MCMCglmm_2.05/R/mult.memb.R unlink MCMCglmm_2.05/R/predict.MCMCglmm.R~ unlink MCMCglmm_2.05/R/KPPM.R unlink MCMCglmm_2.05/R/spl.R unlink MCMCglmm_2.05/R/Dtensor.R unlink MCMCglmm_2.05/R/Ptensor.R unlink MCMCglmm_2.05/R/kunif.R unlink MCMCglmm_2.05/R/residuals.MCMCglmm.R unlink MCMCglmm_2.05/R/mult.memb.R~ unlink MCMCglmm_2.05/R/knorm.R unlink MCMCglmm_2.05/R/MCMCglmm.R~ unlink MCMCglmm_2.05/R/MCMCglmm.R unlink MCMCglmm_2.05/R/SimL.R~ unlink MCMCglmm_2.05/R/list2bdiag.R unlink MCMCglmm_2.05/R/mterms.R~ unlink MCMCglmm_2.05/R/prunePed.R~ unlink MCMCglmm_2.05/R/sm2asreml.R unlink MCMCglmm_2.05/R/plotsubspace.R unlink MCMCglmm_2.05/R/plot.MCMCglmm.R~ unlink MCMCglmm_2.05/R/residuals.MCMCglmm.R~ unlink MCMCglmm_2.05/R/Ecor.R~ unlink MCMCglmm_2.05/R/commutation.R unlink MCMCglmm_2.05/R/getVCV.R~ unlink MCMCglmm_2.05/R/asreml.R~ unlink MCMCglmm_2.05/R/pretty.R~ unlink MCMCglmm_2.05/R/sir.R unlink MCMCglmm_2.05/R/rIW.R unlink MCMCglmm_2.05/R/split.direct.sum.R~ unlink MCMCglmm_2.05/R/Tri2M.R unlink MCMCglmm_2.05/R/find.componets.R~ unlink MCMCglmm_2.05/R/inverseA.R unlink MCMCglmm_2.05/R/MCMCam.R~ unlink MCMCglmm_2.05/R/inverseAnonC.R~ unlink MCMCglmm_2.05/R/posterior.mode.R unlink MCMCglmm_2.05/R/path.R~ unlink MCMCglmm_2.05/R/rIW.R~ unlink MCMCglmm_2.05/R/knorm.R~ unlink MCMCglmm_2.05/R/Dtensor.R~ unlink MCMCglmm_2.05/R/buildZ.R~ unlink MCMCglmm_2.05/R/plotsubspace.R~ unlink MCMCglmm_2.05/R/posterior.mode.R~ unlink MCMCglmm_2.05/R/posterior.cor.R~ unlink MCMCglmm_2.05/R/split.direct.sum.R unlink MCMCglmm_2.05/R/residuals (copy).MCMCglmm.R~ unlink MCMCglmm_2.05/R/Dexpressions.R~ unlink MCMCglmm_2.05/R/Ddivergence.R unlink MCMCglmm_2.05/R/spl.R~ unlink MCMCglmm_2.05/R/Dexpressions.R unlink MCMCglmm_2.05/R/mterms.R unlink MCMCglmm_2.05/R/rtnorm.R unlink MCMCglmm_2.05/R/inverseA.R~ unlink MCMCglmm_2.05/R/find.components.R~ unlink MCMCglmm_2.05/R/posterior.evals.R~ unlink MCMCglmm_2.05/R/multmemb.R~ unlink MCMCglmm_2.05/R/SStest.R~ unlink MCMCglmm_2.05/R/plotprior.R~ unlink MCMCglmm_2.05/R/find.components.R unlink MCMCglmm_2.05/R/MCMCgompSInt.R~ unlink MCMCglmm_2.05/R/dcmvnorm.R~ unlink MCMCglmm_2.05/R/summary.MCMCglmm.R~ unlink MCMCglmm_2.05/R/buildZ.R rmdir MCMCglmm_2.05/R cannot remove directory for /home/jarrod/mnt/shared: Permission denied at /usr/lib64/R/bin/build line 263 cannot remove directory for /home/jarrod/mnt/scieng1: Permission denied at /usr/lib64/R/bin/build line 263 cannot remove directory for /home/jarrod/mnt: Directory not empty at /usr/lib64/R/bin/build line 263 cannot remove directory for /home/jarrod/.gvfs: Device or resource busy at /usr/lib64/R/bin/build line 263 cannot make child directory read-write-exec for /home/jarrod/.local/share/Trash/files/MasterBayes_2.2.4.Rcheck: Operation not permitted at /usr/lib64/R/bin/build line 263 cannot remove directory for /home/jarrod/.local/share/Trash/files: Directory not empty at /usr/lib64/R/bin/build line 263 cannot remove directory for /home/jarrod/.local/share/Trash: Directory not empty at /usr/lib64/R/bin/build line 263 cannot remove directory for /home/jarrod/.local/share: Directory not empty at /usr/lib64/R/bin/build line 263 cannot remove directory for /home/jarrod/.local: Directory not empty at /usr/lib64/R/bin/build line 263 cannot remove directory for /home/jarrod: Permission denied at /usr/lib64/R/bin/build line 263 * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'MCMCglmm_2.05.tar.gz' tar: /home/jarrod/Work/AManal/MCMCglmm_2.05.tar: Cannot open: No such file or directory tar: Error is not recoverable: exiting now gzip: /home/jarrod/Work/AManal/MCMCglmm_2.05.tar: No such file or directory cannot remove path when cwd is /tmp/Rbuild93379662 for /tmp/Rbuild93379662: at /usr/lib64/R/bin/build line 433
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.